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quote from MINIMAUL

"The GOG release of SR2 is absolutely identical in terms of addresses and layout - everything is in exactly the same place. This doesn't happen by accident - it means that it is the same EXE. SR2 on Steam predates CEG - so everyone has the same EXE, it's just encrypted. It decrypts it on every game launch. SR2 didn't have any extra Steam hooks in it - that's how it was offered on a wide variety of stores. So to make the GOG release, they simply took the EXE before it had the Steam encryption applied to it, and used that. "
So the exe and the game's file structure is the same. So what?
There can be all kinds of changes in the files themselves.